\HeaderA{plotSpikeCI}{plot spike concentration vs measured intensity}{plotSpikeCI}
\keyword{hplot}{plotSpikeCI}
\begin{Description}\relax
plot spike known concentration and measured intensity of one array.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSpikeCI(spike, parameter,array = 1, bc = FALSE, area = TRUE, 
            meanpoint = TRUE,xlab = "log(Concentration)",
            ylab = "log(Intensity)", main = colnames(spike$R)[array],
            onlycalib = TRUE, xlim = NULL, ylim = NULL, pch = 19,
            cex = 0.2, meanpch = 21, meancex = 1, lwd = 1.5, 
            cy5col = "red", cy3col = "green", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{spike}] a \code{SpikeList} object.
\item[\code{parameter}] a \code{ParameterList} object.
\item[\code{array}] integer giving the array to be plotted. 
\item[\code{bc}] a logical value. \code{TRUE} means background corrected measured 
intensities are used. Default is FALSE.
\item[\code{area}] a logical value. \code{TRUE} means spot area is used to calculate 
measured intensities. Namly, measured intensities are calculated by 
foreground intensities(or background corrected intensities, if bc is 
\code{TRUE}) multiply spot area. \code{FALSE} means spot area is not used.
Default is \code{TRUE}.
\item[\code{meanpoint}] a logical value. \code{TRUE} is to show meanpoint of measured
intensities with the same concentration on the plot. \code{FALSE} means not show. 
\item[\code{xlab}] a title for the x axis.
\item[\code{ylab}] a title for the y axis.
\item[\code{main}] an overall title for the plot.
\item[\code{onlycalib}] a logical value. \code{TRUE} means only the calibration controls are on 
the plot. \code{FALSE} means to plot all the spikes
\item[\code{xlim}] the x limits (min,max) of the plot.
\item[\code{ylim}] the y limits of the plot.
\item[\code{pch}] a integer code for one of plotting characters or symbols
for the spike data set. Default is 21.
\item[\code{cex}] a numerical value giving the amount by which the points which
indicate spike data set should be scaled relative to the default. Default is 0.4.
\item[\code{meanpch}] a integer code for one of plotting characters or symbols
for the meanpoints. Default is 21.
\item[\code{meancex}] a numerical value giving the amount by which the meanpoints
should be scaled relative to the default value. Default is 1.
\item[\code{lwd}] width of the model curves. Default is 1.5.
\item[\code{cy5col}] color of all symbols for cy5. Default is red.
\item[\code{cy3col}] color of all symbols for cy3. Default is green.
\item[\code{...}] other graphical parameters can be used in function \code{\LinkA{plot}{plot}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function plots spike concentration and measured intensity of one array. 
array number is specified by the argument \code{array}. It accepts the concentration
of given array from the agrument \code{spike}, which is a \code{\LinkA{SpikeList}{SpikeList}}
object. The measured intensities are calculated from \code{spike}. Four different ways can
be used to calculate the measured intensities. Arguments \code{bc} and \code{area} are 
logical and their combinations are used for specifying the four differents ways. 
\code{bc} indicates using background correction or not. \code{area} indicates multipling 
spot area or not. The default value of these two arguments are \code{bc} = FALSE and 
\code{area} = TRUE. 

In order to help data visualization, meanpoints and model curve can be added
on the plot. And the arguments \code{meanpoint} and \code{parameter} are correspond to these.
The meadians of every group of measured intensities which have the same concentration 
are shown on the polt if \code{meanpoint} is true. Model curves of both dye are 
shown if the arguement \code{parameter} is specified after parameter estimation.
\end{Details}
\begin{Value}
A plot is created on the current graphics device.
\end{Value}
\begin{Author}\relax
Hui Zhao
\end{Author}
\begin{SeeAlso}\relax
see graphic functions \code{\LinkA{plot}{plot}}, \code{\LinkA{par}{par}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# load data: spike
data(spike)

# specify the array to be plotted.
array <- 1

# use the default values for other parameters.
plotSpikeCI(spike,array=array)

# after parameter estimation, the model curves can be shown on the plot.
data(parameter)
plotSpikeCI(spike,parameter,array=array)
\end{ExampleCode}
\end{Examples}

